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- EMDB-25678: Structure of dimeric phosphorylated Pediculus humanus (Ph) PINK1 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-25678 | |||||||||
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Title | Structure of dimeric phosphorylated Pediculus humanus (Ph) PINK1 with kinked alpha-C helix in chain B | |||||||||
![]() | Dimer map (locally filtered). Generated from 3D variability analysis and local refinement of the dimer. Initial dimer was generated from local refinement of a dimer from the dodecamer. | |||||||||
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Function / homology | ![]() positive regulation of mitochondrial fission / autophagy / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine/threonine kinase activity / ATP binding ...positive regulation of mitochondrial fission / autophagy / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | |||||||||
![]() | Gan ZY / Leis A / Dewson G / Glukhova A / Komander D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Activation mechanism of PINK1. Authors: Zhong Yan Gan / Sylvie Callegari / Simon A Cobbold / Thomas R Cotton / Michael J Mlodzianoski / Alexander F Schubert / Niall D Geoghegan / Kelly L Rogers / Andrew Leis / Grant Dewson / Alisa ...Authors: Zhong Yan Gan / Sylvie Callegari / Simon A Cobbold / Thomas R Cotton / Michael J Mlodzianoski / Alexander F Schubert / Niall D Geoghegan / Kelly L Rogers / Andrew Leis / Grant Dewson / Alisa Glukhova / David Komander / ![]() ![]() Abstract: Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease. PINK1 has many unique features that enable it to phosphorylate ...Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease. PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin. Structural analysis of PINK1 from diverse insect species with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. Here we elucidate the activation mechanism of PINK1 using crystallography and cryo-electron microscopy (cryo-EM). A crystal structure of unphosphorylated Pediculus humanus corporis (Ph; human body louse) PINK1 resolves an N-terminal helix, revealing the orientation of unphosphorylated yet active PINK1 on the mitochondria. We further provide a cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, as well as a cryo-EM structure of phosphorylated PhPINK1 undergoing a conformational change to an active ubiquitin kinase state. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our research delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.9 KB 19.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.5 KB | Display | ![]() |
Images | ![]() | 64.8 KB | ||
Masks | ![]() | 325 MB | ![]() | |
Others | ![]() ![]() ![]() | 161.4 MB 301.1 MB 301.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 847.7 KB | Display | ![]() |
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Full document | ![]() | 847.3 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t4kMC ![]() 7t3xC ![]() 7t4lC ![]() 7t4mC ![]() 7t4nC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Dimer map (locally filtered). Generated from 3D variability analysis and local refinement of the dimer. Initial dimer was generated from local refinement of a dimer from the dodecamer. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Dimer map (unsharpened).
File | emd_25678_additional_1.map | ||||||||||||
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Annotation | Dimer map (unsharpened). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Dimer half map.
File | emd_25678_half_map_1.map | ||||||||||||
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Annotation | Dimer half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Dimer half map.
File | emd_25678_half_map_2.map | ||||||||||||
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Annotation | Dimer half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dodecameric phosphorylated Pediculus humanus (Ph) PINK1
Entire | Name: Dodecameric phosphorylated Pediculus humanus (Ph) PINK1 |
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Components |
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-Supramolecule #1: Dodecameric phosphorylated Pediculus humanus (Ph) PINK1
Supramolecule | Name: Dodecameric phosphorylated Pediculus humanus (Ph) PINK1 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all Details: Dodecamer was stabilised by hydrogen peroxide treatment prior to phosphorylation and purification by SEC |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Serine/threonine-protein kinase PINK1, putative
Macromolecule | Name: Serine/threonine-protein kinase PINK1, putative / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53.053602 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPSGLLTKDD ELEGICWEIR EAVSKGKWND SESENVEQLQ AANLDELDLG EPIAKGCNAV VYSAKLKNVQ SNKLAHQLAV KMMFNYDVE (SEP)NSTAILKAM YRETVPAMSY FFNQNLFNIE NISDFKIRLP PHPNIVRMYS VFADRIPDLQ CNKQLYP EA LPPRINPEGS ...String: GPSGLLTKDD ELEGICWEIR EAVSKGKWND SESENVEQLQ AANLDELDLG EPIAKGCNAV VYSAKLKNVQ SNKLAHQLAV KMMFNYDVE (SEP)NSTAILKAM YRETVPAMSY FFNQNLFNIE NISDFKIRLP PHPNIVRMYS VFADRIPDLQ CNKQLYP EA LPPRINPEGS GRNMSLFLVM KRYDCTLKEY LRDKTPNMRS SILLLSQLLE AVAHMNIHNI SHRDLKSDNI LVDLSEGD A YPTIVITDFG CCLCDKQNGL VIPYRSEDQD KGGNRALMAP EIANAKPGTF SWLNYKKSDL WAVGAIAYEI FNIDNPFYD KTMKLLSKSY KEEDLPELPD TIPFIIRNLV SNMLSRSTNK RLDCDVAATV AQLYLWAPSS WLKENYTLPN SNEIIQWLLC LSSKVLCER DITARNKTNT MSESVSKAQY KGRRSLPEYE LIASFLRRVR LHLVRKGLKW IQELHIYN |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.3 mg/mL | |||||||||
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Buffer | pH: 8.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.039 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |